If you enter different amounts for your 1099-R for Box 1 and Box 2a, TurboTax asks several questions to determine what is the correct taxable amount.
You could delete that 1099-R and re-enter, paying close attention to the follow-up questions asked after your entry.
Here's more info on Entering Pension or Annuity Distributions and detailed info on Form 1099-R.
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